3RKH

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite (full occupancy)

Summary for 3RKH

• Entry DOI: 10.2210/pdb3rkh/pdb
• Related: 2OT4 3F29
• Descriptor: Eight-heme nitrite reductase, HEME C, NITRITE ION, ... (6 entities in total)
• Functional Keywords: eight hemes c, nitrite reductase, tyr-cys covalent bond, oxidoreductase
• Biological source: Thioalkalivibrio nitratireducens
• Total number of polymer chains: 2
• Total formula weight: 128172.12

Authors

Trofimov, A.A.,Polyakov, K.M.,Tikhonova, T.V.,Tikhonov, A.V.,Dorovatovskii, P.V.,Popov, V.O. (deposition date: 2011-04-18, release date: 2011-06-15, Last modification date: 2023-09-13)

Primary citation

Trofimov, A.A.,Polyakov, K.M.,Tikhonova, T.V.,Tikhonov, A.V.,Safonova, T.N.,Boyko, K.M.,Dorovatovskii, P.V.,Popov, V.O.
Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity.
Acta Crystallogr.,Sect.D, 68:144-153, 2012

PubMed Abstract: Octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR), like the previously characterized pentahaem nitrite reductases (NrfAs), catalyzes the six-electron reductions of nitrite to ammonia and of sulfite to sulfide. The active site of both TvNiR and NrfAs is formed by the lysine-coordinated haem and His, Tyr and Arg residues. The distinguishing structural feature of TvNiR is the presence of a covalent bond between the CE2 atom of the catalytic Tyr303 and the S atom of Cys305, which might be responsible for the higher nitrite reductase activity of TvNiR compared with NrfAs. In the present study, a new modified form of the enzyme (TvNiRb) that contains an additional covalent bond between Tyr303 CE1 and Gln360 CG is reported. Structures of TvNiRb in complexes with phosphate (1.45 Å resolution) and sulfite (1.8 Å resolution), the structure of TvNiR in a complex with nitrite (1.83 Å resolution) and several additional structures were determined. The formation of the second covalent bond by Tyr303 leads to a decrease in both the nitrite and sulfite reductase activities of the enzyme. Tyr303 is located at the exit from the putative proton-transport channel to the active site, which is absent in NrfAs. This is an additional argument in favour of the involvement of Tyr303 as a proton donor in catalysis. The changes in the activity of cytochrome c nitrite reductases owing to the formation of Tyr-Cys and Tyr-Gln bonds may be associated with changes in the pK(a) value of the catalytic tyrosine.

PubMed: 22281743
DOI: 10.1107/S0907444911052632

Experimental method

X-RAY DIFFRACTION (1.83 Å)